That’s because FDA approval for its much-anticipated exenatide LAR diabetes drug could be delayed, according to a filing with the Securities and Exchange Commission.

The agency rejected study data that was meant to show that exenatide LAR batches made by its partner, Alkermes, were equivalent to batches made at Amylin’s own facility in Ohio. The upshot is that, if Amylin has to conduct another study, it would likely delay plans for FDA approval by the middle of 2009. Amylin continuing discussions with the FDA.

Not surprisingly, the disclosure hammered stocks for both companies, since exenatide is supposed to be the follow-up for Byetta. The bad news follows reports in August of six deaths in patients taking its Byetta diabetes med, although the deaths have not been directly linked to the drug. The patients had developed pancreatitis.

BMO Capital Markets analyst Robert Hazlett expects a regulatory filing in either late 2010 or early 2011, the Associated Press writes. “This delay in the exenatide LAR timeline was a risk we had long recognized,” he wrote in an investor note. “An additional study will likely be necessary to demonstrate comparability between the two different manufactured products.”